How Cryo-EM Helped Researchers Uncover the Molecular Structures of the Ebola Virus

Dr. Erica Ollmann Saphire is a leading structural immunologist and a professor at La Jolla Institute for Immunology, where she has set up a state-of-the-art cryo-electron microscopy (cryo-EM) research lab. The recipient of numerous awards, Dr. Saphire and her team have uncovered the molecular structures of the Ebola, Sudan, Bundibugyo, Marburg, LCMV and Lassa virus surface glycoproteins, how these viruses suppress immune function, and where human antibodies dock to defeat these viruses. Dr. Saphire also directs the Viral Haemorrhagic Fever Immunotherapeutic Consortium, composed of 43 academic, industrial and government labs across five continents. We met with Dr. Saphire to learn how cryo-EM is advancing her research.

Q&A with Dr. Saphire about how cryo-EM is advancing Ebola research

This Q&A has been edited for clarity and length.

Accelerating Microscopy (AM): What interests you about immunology at the molecular level?

Dr. Saphire: Immunology is a beautiful and complex science. It’s the science of understanding how your body can heal itself: how, every day, it detects and destroys invaders before you ever know you’ve been infected, as well as cancer cells before they take hold. Immunology can be studied on multiple levels. You can study it at a population level to learn how we develop herd immunity against different diseases. You can study it at a human level to learn how one human has conquered an auto immune disease or fought off an infection and become immune. And, you can study it at the cellular level.

I study it at the far extreme, the molecular level, to learn about pathogens and how immune molecules see each other. It’s at the molecular level where the rubber hits the road. It’s where your immune system can seek out and destroy a pathogen and build that memory so it’s never infected with that pathogen again. We can harness that information to develop vaccines so that you don’t have to worry about new viruses emerging all the time and even to develop vaccines against other diseases such as cancer.

AM: Why did you specifically decide to focus on viruses such as Ebola?

Dr. Saphire: Viruses are fascinating because they can be so simple. While you and I have 20,000 genes, Ebola virus has just seven genes. Despite that, it can cause hundreds of thousands of cases every year. The question is: how can something so simple be so deadly? If the virus is that simple, we can take it apart and examine the vulnerabilities. That’s exactly what we’ve been able to do.

AM: How does the Ebola virus work and how is it contracted?

Dr. Saphire: Viruses come in all different shapes and sizes. Some look like space invaders, while others look like little snowflake-covered balls. The Ebola virus is different: it looks like a strand of spaghetti. And, if you look at an infected cell under an electron microscope, it looks like a ball of spaghetti coming out. Each virus is a long, flexible filament that can adopt different shapes. Its biological mission is to replicate itself and it does so with terrifying speed. At the time of death, a patient can have a billion copies of the virus per cubic centimeter of their blood.

Anybody can become infected if they come into contact with the fluids of an infected person such as blood, diarrhea, semen, or even sweat. The virus can find its way across your own skin barriers or through small cuts or openings in your mouth. It establishes hold and starts replicating inside you. It is extremely lethal. Depending on the type of Ebola virus and the time of outbreak, between 40-90 percent of all people infected will die.

AM: Where are we now in terms of the number of people infected?

Dr. Saphire: From 2014 to 2016 we had the largest ever outbreak of Ebola virus, and it spread from a single infected two-year-old, whom we think played in a hollowed-out tree, to 30,000 people across international borders. We currently have another outbreak that’s added another 3,400 people. Although we have a mobilized vaccine now that’s been given to hundreds of thousands of people, the virus hasn’t stopped and there are a couple of new cases every day. The bottom line is that anywhere there’s regional instability and tens of thousands of refugees or competing factions and distrust of authorities, it’s extremely difficult to stop the virus—any virus.

AM: What limitations were you up against before you incorporated cryo-EM into your research?

Dr. Saphire: The main tool available to us was x-ray crystallography. The way that works is that you have to coax your molecule into forming a three-dimensional crystal, like the sugar crystals that grow on the lip of your old maple syrup bottle. You need a couple hundred thousand to a million copies to line up in a three-dimensional array like soldiers. You can put this crystal in the x-ray beam, scatter the x-rays, and use that to calculate the structure of the molecule. X-ray crystallography is an incredibly powerful technique but there was one fundamental problem for us and that was that the molecules of viruses are mobile. They’re wiggly, they’re covered in sugars, and they don’t want to form solids. With x-ray crystallography, we would spend years working on this problem. It took us five years to crack the structure of Ebola virus and, meanwhile, the virus continued to rage.

AM: How is cryo-EM helping to advance your research?

Dr. Saphire: With cryo-EM, we could directly image the molecules immediately without needing those crystals—and that took a project from five years to ten weeks. That acceleration of time is critical to human health. It doesn’t help to have a cure for a virus three years after the outbreak has already burned out and gone away. You need it right away. These electron microscopes and detectors have also given us the ability to appreciate all of the biological complexity we couldn’t see before. Molecules aren’t all identical. Sometimes they have different sugars attached in different places. Sometimes the sugars are bent more to the left or the right. Sugars that are attached in different places trigger different kinds of immune responses or allow the virus to hide from immune response. That’s information we needed to make a vaccine. If we couldn’t see it, we didn’t know it. We have to be able see the entire biological battle between the virus and immune system—and we have to be able to do that quickly.

AM: What have you learned about the molecular structure of Ebola using cryo-EM, and how has this led to a promising drug?

Dr. Saphire: We learned two things from seeing the structure of the surface protein of Ebola virus. We saw how the surface protein could enter cells by changing its shape to hide and expose different things at different times. We also learned how the immune system could attack the protein in different places and by different geometries. That gave us a starting point to start to tease apart what defenses would and wouldn’t be effective.

Using those molecular structures as the roadmap, we’ve galvanized an unprecedented global collaboration of academic, industry and government scientists working together to pool their expertise and create a large database of information of what constitutes a defense against Ebola virus. We can now predict, with 96 percent accuracy, what will provide protection against a living thing. For the first time, there are lifesaving therapeutics against Ebola virus.

AM: That sounds like a major breakthrough.

Dr. Saphire: It’s a good starting point, but there’s much more to be done. There are six different kinds of Ebola virus, there’s the Marburg virus… there are so many viruses in the world. The first therapy is effective against one type, but what about the next one? What if three or four, or five, viruses break out simultaneously? We need more broadly active therapies—a single shot that’s going to inactive them all. And we need therapies that work at a lower dose so they can be delivered more inexpensively to more people.

AM: What implications does cryo-EM have for the novel coronavirus?

Dr. Saphire: We first heard about the novel coronavirus on December 31 and three weeks later there were already thousands of cases in multiple countries. So, this is something against which science must act quickly. The new tools we have suggest that we’re no longer just going to have to wait and hope, but that we can actually discover what’s different about this virus and where it’s vulnerable—and then deliver something to help in real time.

AM: What is your outlook on cryo-EM and electron microscopy as a way to combat infectious diseases?

Dr. Saphire: Going forward, we’re going to need a range of tools. We’re going to continue to need x-ray crystallography for the high-quality data, the reproducibility, and the ease. We’re going to need cryo-EM to understand the more complex molecules and the ones that don’t crystallize. We need tomography to understand larger structures and subcellular structures. We need biophysics and other techniques to understand how things change that we can’t capture with our structural biology techniques. Additionally, we need scientists who are experts in each one of these techniques and the new methods being developed.

AM: Do you think viruses like Ebola will one day be eradicated?

Dr. Saphire: I do think we can achieve life without many of these diseases. By putting the right people with the right skillsets and tools to focus on these problems, we can achieve life without Ebola, life without malaria, life without Lassa. We can accomplish this by visualizing what the virus is, where it’s vulnerable, and what an effective immune response might be. We can discover and deliver vaccines and therapeutics for broad protection more rapidly than we ever could before.

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